The objective of this work is to advance the state-of-the-art in electrospray/ion trap mass spectrometry of biomolecules by extending its mixture analysis capabilities and its useful range of structural analysis from molecules ranging in mass up to about 2-4 kDa to molecules ranging in mass up to several tens of kiloDaltons. The two major emphasis areas in this work are to improve understanding of the factors that underlie the dissociation behavior of moderately sized proteins (less than 60 kDa) and to develop new experiments for complex bio-polymer mixture analysis based on ion/ion chemistry. This work will permit applications to be considered that involve the direct interrogation of, for example, whole proteins. Such applications might include rapid protein identification, rapid identification of post-translational modifications, rapid analysis of protein variants, etc. The quadrupole ion trap is already a remarkably powerful tool for the manipulation and mass/charge analysis of biologically-derived ions. This work will allow for a dramatic expansion in the size of bio-polymer that can be studied via tandem mass spectrometry with a bench-top instrument. The proposed effort seeks to develop new tools for deriving structural information from high mass ions, with particular emphasis on proteins. Instrumentation will be developed to allow for new studies designed to improve understanding of the ion/ion reactions of proteins and the unimolecular (i.e. dissociation) reactions of proteins. Specifically, new instrumental developments will be made to enhance both the range of ion/ion chemistry that can be studied and to improve the figures of merit of mass analysis of high mass ions.